Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human hepatocellular carcinomas

ABSTRACT: Gene expression profile of Human hepatocellular carcinoma were investigated with spotted cDNA microarray technology. Tumor and non-tumorous region used this experiment were hybridization with normal liver total RNA in same cDNA chip, respectivly. All tests were accompanied with dye-swap normalization.

ORGANISM(S): Homo sapiens

DISEASE(S): hepatocellular carcinoma-non tumorous region

SUBMITTER: Yejin Jang

PROVIDER: E-TABM-423 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Functional and clinical evidence for NDRG2 as a candidate suppressor of liver cancer metastasis.

Lee Dong Chul DC Kang Yun Kyung YK Kim Woo Ho WH Jang Ye Jin YJ Kim Dong Joon DJ Park In Young IY Sohn Bo Hwa BH Sohn Hyun Ahm HA Lee Hee Gu HG Lim Jong Seok JS Kim Jae Wha JW Song Eun Young EY Kim Dong Min DM Lee Mi-Ni MN Oh Goo Taeg GT Kim Soo Jung SJ Park Kyung Chan KC Yoo Hyang Sook HS Choi Jong Young JY Yeom Young Il YI

Cancer research 20080601 11

We searched for potential suppressors of tumor metastasis by identifying the genes that are frequently down-regulated in hepatocellular carcinomas (HCC) while being negatively correlated with clinical parameters relevant to tumor metastasis, and we report here on the identification of N-myc downstream regulated gene 2 (NDRG2) as a promising candidate. NDRG2 expression was significantly reduced in HCC compared with nontumor or normal liver tissues [87.5% (35 of 40) and 62% (62 of 100) at RNA and ...[more]

PMID: 18519680

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Project description:Considerable interest and controversy has arisen over the potential effects of seismic surveys carried out during exploration for oil and gas deposits. Regarding fish, there is a concern that intense sound sources, such as seismic airguns, may injure their auditory system. In this study, salmonid cDNA microarrays, reciprocal suppression subtractive hybridization (SSH) cDNA libraries and quantitative reverse transcription – polymerase chain reaction (QPCR) were used to identify and study a responsive gene set in the inner ear of Atlantic salmon (Salmo salar) following seismic airgun exposure. Microarray analyses on pooled seismic exposed inner ear RNA versus pooled control inner ear RNA revealed 79 unique transcripts (passing background threshold) that were greater than 1.75-fold differentially-regulated by acoustic stress on at least 3 of the 4 slides in the study (including at least one dye-swap). QPCR analyses of 8 microarray-identified transcripts of interest revealed a significant up-regulation (P<0.05) of transcripts encoding nicotinamide riboside kinase 2 (1.89-fold) and hemoglobin subunit alpha-4 (3.78-fold), and a significant down-regulation (P<0.05) of a transcript encoding C14orf159 protein (1.35-fold). QPCR analyses also confirmed an overall up-regulation of transcripts encoding growth hormone I (7.78-fold), c-type lectin receptor A (2.20-fold) and retinol binding protein I (1.24-fold), however these differences were not considered to be statistically significant (P<0.05) due to the high biological variability in the seismic exposed group for these transcripts of interest. A total of 683 expressed sequence tags (ESTs) generated from SSH cDNA salmon ear libraries enriched for genes responsive to seismic airgun noise have been deposited in the GenBank dbEST. Targeted gene discovery in salmon ear allowed for the identification of novel transcripts, including some with sensory-relevant functional annotations, and represents a significant contribution to salmonid hearing research. Initial results demonstrate that genomics has the potential to greatly enhance our understanding of the impact of seismic airguns on gene and molecular pathways involved in hearing, and provide valuable molecular biomarkers that can act as an early warning sensor to acoustic stress. Juvenile Atlantic salmon (Salmo salar) smolt were obtained from North Water Products Ltd., Daniel’s Harbour, NL and held at ambient seawater temperature, in a flow-through system supplied with air at the Northwest Atlantic Fisheries Centre, St. John’s, NL. Two weeks prior to seismic airgun exposures, fish were divided into two 1m3 cages, one each for control (non-exposed) and exposed groups, in a 15,000L aquarium at ambient seawater temperature (0.2°C). Each cage was placed the same distance from the water intake and airstones were placed next to each cage. Fish were fasted for two days prior to exposure. Sixteen control (non-exposed) fish from one cage were sampled prior to seismic activity. Immediately following sampling of control fish, seventeen fish in the remaining cage were placed 2m from a 10in3 Texas Instruments airgun. Fish were subjected to 50 exposures, 1 exposure every 10 seconds, at an average sound pressure level of 204 dB peak-to-peak relative to 1µPa; considered to be a worse case scenario within a few hundred meters of a survey vessel. Seventeen seismic exposed fish were sampled 16 h following exposure. The only aquarium available that was suitable for seismic airgun exposures was not designed to have a regulated photoperiod. For this reason the fish were held under a constant daylight regime. Fish were collected by dip-net and euthanized by severing the spinal cord. The inner ears from each salmon were removed, placed immediately in RNase-free 2 ml tubes, and then flash frozen in liquid nitrogen. RNA isolated from the right inner ear of the 12 seismic exposed and 12 control individuals that gave the highest total RNA yields were used to generate 2 mRNA pools (a “seismic” pool and a “control” pool). Each sample contributed 4.0 µg column purified total RNA to each pool. Comparisons were made for the seismic exposed mRNA pool compared to the control (non-exposed) mRNA pool using the consortium for Genomic Research on All Salmonids Project (cGRASP) 16K (salmonid) cDNA array and the 3DNA Array 900 Detection Kit and instructions (Genisphere). Technical quadruplicate slides including 2 dye-swaps were run for the comparison. Slide GG003_011: Cy5-labeled control ear, Cy3-labeled seismic Slide GG003_012: Cy5-labeled control ear, Cy3-labeled seismic Slide GG003_013: Cy3-labeled control ear, Cy5-labeled seismic Slide GG003_014: Cy3-labeled control ear, Cy5-labeled seismic

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Dataset Information

Transcription profiling of human hepatocellular carcinomas

Publications

Functional and clinical evidence for NDRG2 as a candidate suppressor of liver cancer metastasis.

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